scobra is a supplementary package for COBRApy. This version is specifically for Python 3.6 and above.
To install scobra, run this line:
pip install scobra
scobra - an extension of cobrapy
License: MIT License
model.Optimal() doesn't work now because "model.solution.f" doesn't exist any more
currently the ConstraintScan has MinFlux=True option which uses MinFluxSolve. It would be good to add allow to user to choose MinFluxSolve(cobra=True). Currently the default is False and there is no option to make it True.
Would be good to implement both:
i) Add an option to allow user to choose cobra=True when MinFlux=True
ii) make cobra=True the default
The old version of scobra (available in our Frontiers dfba paper's supplementary) works (Windows 10) but latest (downloaded from github recently in virtualbox Ubuntu linux) not working. This problem happens with MinFluxSolve in the latest scobra but not in the old version. In old version after infeasible, codes continues for next iteration. I will try to update again.
Error:
/usr/local/lib/python2.7/dist-packages/cobra/util/solver.pyc in assert_optimal(model, message)
423 """
424 if model.solver.status != optlang.interface.OPTIMAL:
--> 425 raise OPTLANG_TO_EXCEPTIONS_DICTmodel.solver.status
Infeasible: None
From Rahul: I have a small suggestion, instead of printing extra 'no solution', 'no solution found' (even PrintStatus=False) just printing solver status should be fine (should be default). Also I am not sure about the difference between 'no solution' and 'no solution found'. I saw PrintStatus=True is default in MinFluxSolve, but not working (only shows 'no solution', and 'no solution found'; no printing of 'optimal' or 'infeasible').
Min and Max values are flipped in FVA results
Problem with exporting SBML file, e.g. https://static-content.springer.com/esm/art%3A10.1038%2Fs41477-018-0112-2/MediaObjects/41477_2018_112_MOESM3_ESM.xml
Potentially because of wrong default arguments used.
fva.AsMtx() doesn't give a matrix object
model.GetSol() doesn't give a flux object (only an empty dictionary) when there is no solution
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